MobleyLab / benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
☆42Updated 3 years ago
Alternatives and similar repositories for benchmarksets:
Users that are interested in benchmarksets are comparing it to the libraries listed below
- ☆43Updated 3 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆63Updated this week
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆64Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 5 months ago
- A fast solver for large scale MBAR/UWHAM equations☆38Updated 5 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆66Updated this week
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆52Updated 9 months ago
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- ☆21Updated 4 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated last year
- Experimental small molecule hydration free energy dataset☆30Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 4 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 5 months ago
- OpenMM plugin to interface with PLUMED☆65Updated 3 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Physical validation of molecular simulations☆56Updated last month
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆122Updated 2 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆75Updated 8 months ago
- Benchmark set for relative free energy calculations.☆104Updated 8 months ago
- Advanced toolkit for binding free energy calculations☆32Updated last month
- 📐 Symmetry-corrected RMSD in Python☆91Updated 3 months ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆32Updated last week
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 7 months ago
- A comprehensive toolkit for predicting free energies☆51Updated last month
- ☆64Updated last year
- Package for consistent reporting of relative free energy results☆37Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆29Updated 5 years ago
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago